Starting phenix.real_space_refine on Wed Mar 5 20:48:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eog_19854/03_2025/9eog_19854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eog_19854/03_2025/9eog_19854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eog_19854/03_2025/9eog_19854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eog_19854/03_2025/9eog_19854.map" model { file = "/net/cci-nas-00/data/ceres_data/9eog_19854/03_2025/9eog_19854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eog_19854/03_2025/9eog_19854.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.88, per 1000 atoms: 0.82 Number of scatterers: 3522 At special positions: 0 Unit cell: (74.984, 153.264, 37.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 666 8.00 N 648 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 388.2 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 59.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.494A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.347A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 330 removed outlier: 8.880A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N ASN B 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY A 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS B 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY F 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN E 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 346 removed outlier: 6.859A pdb=" N VAL B 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 338 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 340 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER B 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 342 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU F 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER E 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 344 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS E 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE F 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 362 removed outlier: 8.868A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS F 353 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY F 355 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.493A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB2, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.808A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 346 removed outlier: 9.035A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 362 removed outlier: 6.867A pdb=" N SER C 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS D 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY D 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE D 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 58 hydrogen bonds defined for protein. 174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 843 1.33 - 1.45: 816 1.45 - 1.57: 1911 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.307 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.78e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.76e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 3834 1.74 - 3.48: 678 3.48 - 5.21: 228 5.21 - 6.95: 36 6.95 - 8.69: 6 Bond angle restraints: 4782 Sorted by residual: angle pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 111.63 120.32 -8.69 1.36e+00 5.41e-01 4.08e+01 angle pdb=" C ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta sigma weight residual 111.63 120.31 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 111.63 120.30 -8.67 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG E 349 " pdb=" CA ARG E 349 " pdb=" CB ARG E 349 " ideal model delta sigma weight residual 111.63 120.29 -8.66 1.36e+00 5.41e-01 4.05e+01 angle pdb=" C ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta sigma weight residual 111.63 120.28 -8.65 1.36e+00 5.41e-01 4.05e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.95: 1664 9.95 - 19.91: 358 19.91 - 29.86: 102 29.86 - 39.81: 30 39.81 - 49.76: 24 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL E 318 " pdb=" C VAL E 318 " pdb=" N THR E 319 " pdb=" CA THR E 319 " ideal model delta harmonic sigma weight residual 180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual 180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.080: 251 0.080 - 0.158: 241 0.158 - 0.236: 36 0.236 - 0.314: 0 0.314 - 0.391: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 366 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY B 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY B 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 366 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY E 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY E 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY E 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 366 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY C 366 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY C 366 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY C 367 " 0.021 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 1428 2.94 - 3.43: 3246 3.43 - 3.92: 5599 3.92 - 4.41: 5642 4.41 - 4.90: 11553 Nonbonded interactions: 27468 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.445 3.040 ... (remaining 27463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 3576 Z= 0.594 Angle : 1.628 8.689 4782 Z= 1.047 Chirality : 0.104 0.391 534 Planarity : 0.011 0.039 612 Dihedral : 12.855 49.764 1374 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.48 % Allowed : 4.48 % Favored : 91.04 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS E 330 PHE 0.049 0.009 PHE C 346 TYR 0.049 0.017 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.377 Fit side-chains REVERT: A 311 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8059 (ttpt) REVERT: A 317 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8197 (pttt) REVERT: A 321 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (tppp) REVERT: A 331 LYS cc_start: 0.8749 (mttp) cc_final: 0.8450 (mtpm) REVERT: A 342 GLU cc_start: 0.8452 (tt0) cc_final: 0.8212 (mm-30) REVERT: A 375 LYS cc_start: 0.8509 (tttt) cc_final: 0.7763 (mptm) REVERT: B 311 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7985 (mmtt) REVERT: B 316 SER cc_start: 0.9441 (p) cc_final: 0.9163 (p) REVERT: B 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8218 (ptpt) REVERT: B 331 LYS cc_start: 0.8732 (mttp) cc_final: 0.7249 (tmtt) REVERT: B 349 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7733 (ptm160) REVERT: B 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.7672 (mptm) REVERT: C 311 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8030 (mmtt) REVERT: C 317 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8203 (ptmt) REVERT: C 331 LYS cc_start: 0.8796 (mttp) cc_final: 0.8470 (mtpm) REVERT: C 375 LYS cc_start: 0.8454 (tttt) cc_final: 0.7748 (mptm) REVERT: D 311 LYS cc_start: 0.8741 (tmtt) cc_final: 0.7754 (pptt) REVERT: D 317 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8384 (ptmt) REVERT: D 331 LYS cc_start: 0.8844 (mttp) cc_final: 0.8523 (mtpt) REVERT: D 375 LYS cc_start: 0.8954 (tttt) cc_final: 0.8356 (mttm) REVERT: E 311 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8144 (ttmt) REVERT: E 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8149 (ptmt) REVERT: E 321 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: E 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8575 (mtpt) REVERT: E 342 GLU cc_start: 0.8582 (tt0) cc_final: 0.8130 (mm-30) REVERT: E 375 LYS cc_start: 0.8655 (tttt) cc_final: 0.7951 (mttm) REVERT: F 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.7759 (pptt) REVERT: F 331 LYS cc_start: 0.8888 (mttp) cc_final: 0.8627 (mtpt) REVERT: F 375 LYS cc_start: 0.8865 (tttt) cc_final: 0.8486 (mtpm) outliers start: 18 outliers final: 1 residues processed: 140 average time/residue: 1.5077 time to fit residues: 215.4829 Evaluate side-chains 131 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 351 GLN A 374 HIS B 307 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 374 HIS C 307 GLN C 330 HIS C 351 GLN C 374 HIS D 307 GLN D 336 GLN D 351 GLN D 368 ASN D 374 HIS E 307 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 307 GLN F 368 ASN F 374 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124886 restraints weight = 4156.535| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.58 r_work: 0.3821 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3576 Z= 0.284 Angle : 0.664 5.523 4782 Z= 0.339 Chirality : 0.054 0.160 534 Planarity : 0.004 0.027 612 Dihedral : 6.216 30.899 484 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.74 % Allowed : 16.92 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.021 0.003 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.408 Fit side-chains REVERT: A 317 LYS cc_start: 0.8113 (ptpp) cc_final: 0.7882 (ptmm) REVERT: A 348 ASP cc_start: 0.7492 (t0) cc_final: 0.7147 (m-30) REVERT: B 311 LYS cc_start: 0.8281 (tmtt) cc_final: 0.7731 (mmtt) REVERT: B 317 LYS cc_start: 0.8444 (ptpp) cc_final: 0.7996 (ptmt) REVERT: B 331 LYS cc_start: 0.8632 (mttp) cc_final: 0.8231 (mtpt) REVERT: B 358 ASP cc_start: 0.8635 (p0) cc_final: 0.8078 (p0) REVERT: C 317 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7814 (ptmt) REVERT: C 331 LYS cc_start: 0.8745 (mttp) cc_final: 0.8323 (mtpm) REVERT: C 348 ASP cc_start: 0.7702 (t0) cc_final: 0.7451 (m-30) REVERT: C 358 ASP cc_start: 0.8180 (p0) cc_final: 0.7727 (p0) REVERT: D 311 LYS cc_start: 0.8532 (tmtt) cc_final: 0.7568 (pptt) REVERT: D 317 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8127 (ptmt) REVERT: D 331 LYS cc_start: 0.8838 (mttp) cc_final: 0.8157 (mtpt) REVERT: D 340 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8343 (mttm) REVERT: D 347 LYS cc_start: 0.8329 (ptmt) cc_final: 0.7737 (ptmt) REVERT: D 348 ASP cc_start: 0.8065 (t0) cc_final: 0.7800 (m-30) REVERT: D 358 ASP cc_start: 0.8507 (p0) cc_final: 0.8163 (p0) REVERT: D 375 LYS cc_start: 0.8611 (tttt) cc_final: 0.7967 (mttm) REVERT: E 311 LYS cc_start: 0.8213 (tmtt) cc_final: 0.7829 (ttmt) REVERT: E 317 LYS cc_start: 0.8127 (ptpp) cc_final: 0.7588 (ptmt) REVERT: E 331 LYS cc_start: 0.8834 (mttp) cc_final: 0.8279 (mtpt) REVERT: E 340 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7968 (mttm) REVERT: E 348 ASP cc_start: 0.7588 (t0) cc_final: 0.7354 (m-30) REVERT: E 358 ASP cc_start: 0.8073 (p0) cc_final: 0.7682 (p0) REVERT: E 375 LYS cc_start: 0.8373 (tttt) cc_final: 0.7567 (mttp) REVERT: F 311 LYS cc_start: 0.8434 (tmtt) cc_final: 0.7585 (pptt) REVERT: F 317 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8289 (ptmt) REVERT: F 331 LYS cc_start: 0.8909 (mttp) cc_final: 0.8548 (mtpt) REVERT: F 340 LYS cc_start: 0.8652 (mttt) cc_final: 0.8351 (mttm) REVERT: F 348 ASP cc_start: 0.8093 (t0) cc_final: 0.7889 (m-30) REVERT: F 358 ASP cc_start: 0.8336 (p0) cc_final: 0.8103 (p0) outliers start: 11 outliers final: 1 residues processed: 120 average time/residue: 1.2556 time to fit residues: 154.7347 Evaluate side-chains 108 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.142235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.122615 restraints weight = 4143.125| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.51 r_work: 0.3802 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3576 Z= 0.284 Angle : 0.628 6.051 4782 Z= 0.312 Chirality : 0.053 0.145 534 Planarity : 0.004 0.026 612 Dihedral : 5.274 30.763 476 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.24 % Allowed : 21.14 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.019 0.002 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.413 Fit side-chains REVERT: A 311 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7798 (ttpt) REVERT: A 317 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7924 (ptmm) REVERT: A 331 LYS cc_start: 0.8620 (mttp) cc_final: 0.8207 (mtpm) REVERT: A 340 LYS cc_start: 0.8524 (ttmm) cc_final: 0.7977 (mttm) REVERT: A 348 ASP cc_start: 0.7546 (t0) cc_final: 0.7259 (m-30) REVERT: A 375 LYS cc_start: 0.8179 (tttt) cc_final: 0.7505 (mttm) REVERT: B 311 LYS cc_start: 0.8258 (tmtt) cc_final: 0.7696 (mmtm) REVERT: B 317 LYS cc_start: 0.8456 (ptpp) cc_final: 0.8031 (ptmt) REVERT: B 331 LYS cc_start: 0.8680 (mttp) cc_final: 0.8344 (mtmt) REVERT: B 358 ASP cc_start: 0.8681 (p0) cc_final: 0.8315 (p0) REVERT: C 317 LYS cc_start: 0.8237 (ptpp) cc_final: 0.7781 (ptmt) REVERT: C 331 LYS cc_start: 0.8746 (mttp) cc_final: 0.8267 (mtpt) REVERT: C 358 ASP cc_start: 0.8182 (p0) cc_final: 0.7578 (p0) REVERT: D 311 LYS cc_start: 0.8502 (tmtt) cc_final: 0.7583 (pptt) REVERT: D 317 LYS cc_start: 0.8609 (ptpp) cc_final: 0.8029 (ptmm) REVERT: D 331 LYS cc_start: 0.8806 (mttp) cc_final: 0.8269 (mtpt) REVERT: D 340 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8407 (mttp) REVERT: D 347 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7692 (ptmt) REVERT: D 349 ARG cc_start: 0.7572 (ptm160) cc_final: 0.5480 (ppt170) REVERT: D 358 ASP cc_start: 0.8374 (p0) cc_final: 0.8145 (p0) REVERT: D 375 LYS cc_start: 0.8670 (tttt) cc_final: 0.7996 (mttm) REVERT: E 311 LYS cc_start: 0.8200 (tmtt) cc_final: 0.7825 (ttmt) REVERT: E 331 LYS cc_start: 0.8812 (mttp) cc_final: 0.8284 (mtpt) REVERT: E 348 ASP cc_start: 0.7580 (t0) cc_final: 0.7309 (m-30) REVERT: E 358 ASP cc_start: 0.7840 (p0) cc_final: 0.7493 (p0) REVERT: F 311 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7543 (pptt) REVERT: F 317 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8224 (ptmt) REVERT: F 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8671 (mtpt) REVERT: F 340 LYS cc_start: 0.8686 (mttt) cc_final: 0.8295 (mttp) REVERT: F 358 ASP cc_start: 0.8186 (p0) cc_final: 0.7941 (p0) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 1.3807 time to fit residues: 145.7268 Evaluate side-chains 100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.139935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.119137 restraints weight = 4215.962| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.64 r_work: 0.3746 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3576 Z= 0.358 Angle : 0.654 6.771 4782 Z= 0.324 Chirality : 0.053 0.148 534 Planarity : 0.004 0.027 612 Dihedral : 5.260 29.814 476 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.74 % Allowed : 20.65 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.019 0.002 PHE E 346 TYR 0.016 0.004 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.423 Fit side-chains REVERT: A 311 LYS cc_start: 0.8290 (tttt) cc_final: 0.7921 (ttpt) REVERT: A 317 LYS cc_start: 0.8297 (ptpp) cc_final: 0.8081 (ptmm) REVERT: A 331 LYS cc_start: 0.8688 (mttp) cc_final: 0.8340 (mtpm) REVERT: A 348 ASP cc_start: 0.7666 (t0) cc_final: 0.7399 (m-30) REVERT: A 375 LYS cc_start: 0.8192 (tttt) cc_final: 0.7521 (mttm) REVERT: B 311 LYS cc_start: 0.8314 (tttt) cc_final: 0.7804 (mmtt) REVERT: B 317 LYS cc_start: 0.8472 (ptpp) cc_final: 0.8074 (ptmt) REVERT: B 331 LYS cc_start: 0.8725 (mttp) cc_final: 0.8402 (mtpt) REVERT: B 358 ASP cc_start: 0.8699 (p0) cc_final: 0.8323 (p0) REVERT: C 311 LYS cc_start: 0.8398 (tttt) cc_final: 0.7864 (mmtt) REVERT: C 317 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7952 (ptmt) REVERT: C 331 LYS cc_start: 0.8857 (mttp) cc_final: 0.8452 (mtpt) REVERT: C 375 LYS cc_start: 0.8081 (tttt) cc_final: 0.7371 (mttm) REVERT: D 311 LYS cc_start: 0.8552 (tttt) cc_final: 0.7634 (pptt) REVERT: D 317 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8078 (ptmt) REVERT: D 331 LYS cc_start: 0.8860 (mttp) cc_final: 0.8360 (mtpt) REVERT: D 340 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8500 (mttp) REVERT: D 349 ARG cc_start: 0.7639 (ptm160) cc_final: 0.5348 (ppt170) REVERT: D 358 ASP cc_start: 0.8420 (p0) cc_final: 0.8203 (p0) REVERT: D 375 LYS cc_start: 0.8646 (tttt) cc_final: 0.8001 (mttp) REVERT: E 311 LYS cc_start: 0.8301 (tttt) cc_final: 0.7945 (ttmt) REVERT: E 331 LYS cc_start: 0.8885 (mttp) cc_final: 0.8398 (mtpt) REVERT: E 348 ASP cc_start: 0.7765 (t0) cc_final: 0.7437 (m-30) REVERT: F 311 LYS cc_start: 0.8499 (tttt) cc_final: 0.7630 (pptt) REVERT: F 331 LYS cc_start: 0.9028 (mttp) cc_final: 0.8721 (mtpt) REVERT: F 340 LYS cc_start: 0.8712 (mttt) cc_final: 0.8364 (mttp) REVERT: F 358 ASP cc_start: 0.8328 (p0) cc_final: 0.8097 (p0) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 1.4276 time to fit residues: 144.7425 Evaluate side-chains 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.0050 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.144684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124090 restraints weight = 4106.838| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.57 r_work: 0.3803 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3576 Z= 0.227 Angle : 0.602 7.990 4782 Z= 0.291 Chirality : 0.051 0.137 534 Planarity : 0.003 0.025 612 Dihedral : 4.905 32.953 476 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.74 % Allowed : 21.39 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.014 0.002 PHE E 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.406 Fit side-chains REVERT: A 317 LYS cc_start: 0.8229 (ptpp) cc_final: 0.8001 (ptmm) REVERT: A 331 LYS cc_start: 0.8630 (mttp) cc_final: 0.8287 (mtpm) REVERT: A 348 ASP cc_start: 0.7574 (t0) cc_final: 0.7269 (m-30) REVERT: B 311 LYS cc_start: 0.8275 (tttt) cc_final: 0.7712 (mmtt) REVERT: B 317 LYS cc_start: 0.8432 (ptpp) cc_final: 0.8038 (ptmt) REVERT: B 331 LYS cc_start: 0.8726 (mttp) cc_final: 0.8391 (mtpt) REVERT: B 358 ASP cc_start: 0.8637 (p0) cc_final: 0.8269 (p0) REVERT: C 317 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7898 (ptmt) REVERT: C 331 LYS cc_start: 0.8830 (mttp) cc_final: 0.8420 (mtpt) REVERT: C 356 SER cc_start: 0.8781 (p) cc_final: 0.8566 (m) REVERT: D 311 LYS cc_start: 0.8462 (tttt) cc_final: 0.7526 (pptt) REVERT: D 317 LYS cc_start: 0.8565 (ptpp) cc_final: 0.7974 (ptmt) REVERT: D 331 LYS cc_start: 0.8795 (mttp) cc_final: 0.8385 (mtpt) REVERT: D 340 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8393 (mttp) REVERT: D 349 ARG cc_start: 0.7582 (ptm160) cc_final: 0.5278 (ppt170) REVERT: D 358 ASP cc_start: 0.8346 (p0) cc_final: 0.8135 (p0) REVERT: D 375 LYS cc_start: 0.8619 (tttt) cc_final: 0.7989 (mttp) REVERT: E 311 LYS cc_start: 0.8190 (tttt) cc_final: 0.7849 (ttmt) REVERT: E 331 LYS cc_start: 0.8818 (mttp) cc_final: 0.8335 (mtpt) REVERT: E 348 ASP cc_start: 0.7657 (t0) cc_final: 0.7380 (m-30) REVERT: F 311 LYS cc_start: 0.8463 (tttt) cc_final: 0.7557 (pptt) REVERT: F 317 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8150 (ptmt) REVERT: F 331 LYS cc_start: 0.8941 (mttp) cc_final: 0.8642 (mtpt) REVERT: F 340 LYS cc_start: 0.8676 (mttt) cc_final: 0.8260 (mttp) REVERT: F 370 LYS cc_start: 0.8706 (tttp) cc_final: 0.8466 (tttt) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 1.3594 time to fit residues: 129.5470 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 2.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.144138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.124440 restraints weight = 4226.380| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.49 r_work: 0.3829 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3576 Z= 0.289 Angle : 0.627 8.473 4782 Z= 0.303 Chirality : 0.052 0.146 534 Planarity : 0.003 0.025 612 Dihedral : 4.903 31.630 476 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.99 % Allowed : 21.14 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.017 0.002 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.414 Fit side-chains REVERT: A 311 LYS cc_start: 0.8198 (tttt) cc_final: 0.7822 (ttpt) REVERT: A 317 LYS cc_start: 0.8274 (ptpp) cc_final: 0.8060 (ptmm) REVERT: A 331 LYS cc_start: 0.8631 (mttp) cc_final: 0.8071 (mtpt) REVERT: A 348 ASP cc_start: 0.7606 (t0) cc_final: 0.7335 (m-30) REVERT: A 375 LYS cc_start: 0.8245 (tttt) cc_final: 0.7580 (mttm) REVERT: B 311 LYS cc_start: 0.8262 (tttt) cc_final: 0.7738 (mmtt) REVERT: B 317 LYS cc_start: 0.8476 (ptpp) cc_final: 0.8082 (ptmt) REVERT: B 331 LYS cc_start: 0.8719 (mttp) cc_final: 0.8358 (mtpt) REVERT: B 358 ASP cc_start: 0.8626 (p0) cc_final: 0.8228 (p0) REVERT: C 311 LYS cc_start: 0.8348 (tttt) cc_final: 0.7822 (mmtt) REVERT: C 317 LYS cc_start: 0.8360 (ptpp) cc_final: 0.7902 (ptmt) REVERT: C 331 LYS cc_start: 0.8794 (mttp) cc_final: 0.8389 (mtpt) REVERT: C 356 SER cc_start: 0.8815 (p) cc_final: 0.8602 (m) REVERT: C 375 LYS cc_start: 0.8096 (tttt) cc_final: 0.7349 (mttm) REVERT: D 311 LYS cc_start: 0.8476 (tttt) cc_final: 0.7560 (pptt) REVERT: D 317 LYS cc_start: 0.8583 (ptpp) cc_final: 0.7989 (ptmt) REVERT: D 331 LYS cc_start: 0.8874 (mttp) cc_final: 0.8404 (mtpt) REVERT: D 340 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8519 (mttp) REVERT: D 349 ARG cc_start: 0.7645 (ptm160) cc_final: 0.5288 (ppt170) REVERT: D 375 LYS cc_start: 0.8598 (tttt) cc_final: 0.8004 (mttp) REVERT: E 311 LYS cc_start: 0.8181 (tttt) cc_final: 0.7828 (ttmt) REVERT: E 331 LYS cc_start: 0.8828 (mttp) cc_final: 0.8338 (mtpt) REVERT: F 311 LYS cc_start: 0.8412 (tttt) cc_final: 0.7519 (pptt) REVERT: F 317 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8127 (ptmt) REVERT: F 331 LYS cc_start: 0.8983 (mttp) cc_final: 0.8702 (mtpt) REVERT: F 338 GLU cc_start: 0.8561 (tt0) cc_final: 0.8327 (tt0) REVERT: F 340 LYS cc_start: 0.8714 (mttt) cc_final: 0.8312 (mttp) REVERT: F 358 ASP cc_start: 0.8192 (p0) cc_final: 0.7961 (m-30) REVERT: F 370 LYS cc_start: 0.8694 (tttp) cc_final: 0.8451 (tttt) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 1.4254 time to fit residues: 144.4231 Evaluate side-chains 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.142624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.123036 restraints weight = 4184.080| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.45 r_work: 0.3811 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3576 Z= 0.326 Angle : 0.655 8.957 4782 Z= 0.315 Chirality : 0.052 0.150 534 Planarity : 0.004 0.032 612 Dihedral : 4.931 31.261 476 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.24 % Allowed : 21.39 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.018 0.002 PHE E 346 TYR 0.015 0.004 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.382 Fit side-chains REVERT: A 311 LYS cc_start: 0.8186 (tttt) cc_final: 0.7808 (ttpt) REVERT: A 317 LYS cc_start: 0.8261 (ptpp) cc_final: 0.8047 (ptmm) REVERT: A 331 LYS cc_start: 0.8667 (mttp) cc_final: 0.8111 (mtpt) REVERT: A 348 ASP cc_start: 0.7616 (t0) cc_final: 0.7332 (m-30) REVERT: A 375 LYS cc_start: 0.8257 (tttt) cc_final: 0.7600 (mttm) REVERT: B 311 LYS cc_start: 0.8278 (tttt) cc_final: 0.7746 (mmtt) REVERT: B 317 LYS cc_start: 0.8471 (ptpp) cc_final: 0.8057 (ptmt) REVERT: B 331 LYS cc_start: 0.8730 (mttp) cc_final: 0.8357 (mtpt) REVERT: B 358 ASP cc_start: 0.8655 (p0) cc_final: 0.8292 (p0) REVERT: C 311 LYS cc_start: 0.8366 (tttt) cc_final: 0.7831 (mmtt) REVERT: C 317 LYS cc_start: 0.8349 (ptpp) cc_final: 0.7906 (ptmt) REVERT: C 331 LYS cc_start: 0.8765 (mttp) cc_final: 0.8348 (mtpt) REVERT: C 356 SER cc_start: 0.8808 (p) cc_final: 0.8548 (m) REVERT: C 375 LYS cc_start: 0.8072 (tttt) cc_final: 0.7356 (mttm) REVERT: D 311 LYS cc_start: 0.8479 (tttt) cc_final: 0.7568 (pptt) REVERT: D 317 LYS cc_start: 0.8607 (ptpp) cc_final: 0.7993 (ptmt) REVERT: D 331 LYS cc_start: 0.8897 (mttp) cc_final: 0.8389 (mtpt) REVERT: D 340 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8537 (mttp) REVERT: D 349 ARG cc_start: 0.7643 (ptm160) cc_final: 0.5188 (ppt170) REVERT: D 375 LYS cc_start: 0.8590 (tttt) cc_final: 0.8002 (mttp) REVERT: E 311 LYS cc_start: 0.8219 (tttt) cc_final: 0.7860 (ttmt) REVERT: E 331 LYS cc_start: 0.8845 (mttp) cc_final: 0.8333 (mtpt) REVERT: E 369 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8709 (ptpp) REVERT: F 311 LYS cc_start: 0.8456 (tttt) cc_final: 0.7544 (pptt) REVERT: F 331 LYS cc_start: 0.9002 (mttp) cc_final: 0.8684 (mtpt) REVERT: F 338 GLU cc_start: 0.8556 (tt0) cc_final: 0.8334 (tt0) REVERT: F 340 LYS cc_start: 0.8717 (mttt) cc_final: 0.8319 (mttp) REVERT: F 358 ASP cc_start: 0.8166 (p0) cc_final: 0.7891 (m-30) REVERT: F 370 LYS cc_start: 0.8704 (tttp) cc_final: 0.8450 (tttt) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 1.5224 time to fit residues: 155.6333 Evaluate side-chains 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.0970 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.149178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.129685 restraints weight = 4106.701| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.46 r_work: 0.3898 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3576 Z= 0.184 Angle : 0.614 9.084 4782 Z= 0.287 Chirality : 0.050 0.134 534 Planarity : 0.003 0.036 612 Dihedral : 4.642 35.303 476 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.74 % Allowed : 22.14 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.010 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.412 Fit side-chains REVERT: A 317 LYS cc_start: 0.8246 (ptpp) cc_final: 0.7980 (ptmm) REVERT: A 331 LYS cc_start: 0.8599 (mttp) cc_final: 0.8293 (mtpm) REVERT: B 311 LYS cc_start: 0.8271 (tttt) cc_final: 0.7735 (mmtt) REVERT: B 317 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8112 (ptmt) REVERT: B 331 LYS cc_start: 0.8693 (mttp) cc_final: 0.8352 (mtpt) REVERT: B 358 ASP cc_start: 0.8574 (p0) cc_final: 0.8179 (p0) REVERT: C 317 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7910 (ptmt) REVERT: C 331 LYS cc_start: 0.8743 (mttp) cc_final: 0.8356 (mtpt) REVERT: C 356 SER cc_start: 0.8795 (p) cc_final: 0.8567 (m) REVERT: C 375 LYS cc_start: 0.8066 (tttt) cc_final: 0.7390 (mttm) REVERT: D 311 LYS cc_start: 0.8416 (tttt) cc_final: 0.7521 (pptt) REVERT: D 317 LYS cc_start: 0.8568 (ptpp) cc_final: 0.7968 (ptmt) REVERT: D 331 LYS cc_start: 0.8806 (mttp) cc_final: 0.8313 (mtpt) REVERT: D 340 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8429 (mttp) REVERT: D 349 ARG cc_start: 0.7660 (ptm160) cc_final: 0.5260 (ppt170) REVERT: D 353 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8435 (ttpp) REVERT: D 375 LYS cc_start: 0.8575 (tttt) cc_final: 0.8010 (mttp) REVERT: E 311 LYS cc_start: 0.8087 (tttt) cc_final: 0.7770 (ttmt) REVERT: E 331 LYS cc_start: 0.8793 (mttp) cc_final: 0.8336 (mtpt) REVERT: F 311 LYS cc_start: 0.8448 (tttt) cc_final: 0.7569 (pptt) REVERT: F 317 LYS cc_start: 0.8387 (ptpt) cc_final: 0.7968 (ptmt) REVERT: F 331 LYS cc_start: 0.8908 (mttp) cc_final: 0.8613 (mtpt) REVERT: F 340 LYS cc_start: 0.8676 (mttt) cc_final: 0.8271 (mttp) REVERT: F 370 LYS cc_start: 0.8682 (tttp) cc_final: 0.8452 (tttt) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 1.4160 time to fit residues: 136.2785 Evaluate side-chains 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.129592 restraints weight = 4045.536| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.45 r_work: 0.3904 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3576 Z= 0.182 Angle : 0.615 9.278 4782 Z= 0.286 Chirality : 0.050 0.136 534 Planarity : 0.003 0.041 612 Dihedral : 4.546 35.696 476 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.99 % Allowed : 23.38 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.010 0.001 PHE E 346 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.379 Fit side-chains REVERT: A 317 LYS cc_start: 0.8231 (ptpp) cc_final: 0.7987 (ptmm) REVERT: A 331 LYS cc_start: 0.8584 (mttp) cc_final: 0.8077 (mtpt) REVERT: A 375 LYS cc_start: 0.8219 (tttt) cc_final: 0.7581 (mttm) REVERT: B 311 LYS cc_start: 0.8260 (tttt) cc_final: 0.7727 (mmtt) REVERT: B 317 LYS cc_start: 0.8487 (ptpp) cc_final: 0.8093 (ptmt) REVERT: B 331 LYS cc_start: 0.8693 (mttp) cc_final: 0.8374 (mtpt) REVERT: B 358 ASP cc_start: 0.8560 (p0) cc_final: 0.8203 (p0) REVERT: C 317 LYS cc_start: 0.8369 (ptpp) cc_final: 0.7916 (ptmt) REVERT: C 331 LYS cc_start: 0.8745 (mttp) cc_final: 0.8317 (mtpt) REVERT: C 356 SER cc_start: 0.8801 (p) cc_final: 0.8558 (m) REVERT: C 375 LYS cc_start: 0.8101 (tttt) cc_final: 0.7434 (mttm) REVERT: D 311 LYS cc_start: 0.8382 (tttt) cc_final: 0.7515 (pptt) REVERT: D 317 LYS cc_start: 0.8566 (ptpp) cc_final: 0.7981 (ptmt) REVERT: D 331 LYS cc_start: 0.8821 (mttp) cc_final: 0.8335 (mtpt) REVERT: D 340 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8383 (mttt) REVERT: D 353 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8447 (ttpp) REVERT: D 375 LYS cc_start: 0.8571 (tttt) cc_final: 0.8031 (mttp) REVERT: E 311 LYS cc_start: 0.8090 (tttt) cc_final: 0.7793 (ttmt) REVERT: E 331 LYS cc_start: 0.8799 (mttp) cc_final: 0.8367 (mtpt) REVERT: E 356 SER cc_start: 0.8800 (m) cc_final: 0.8485 (t) REVERT: F 311 LYS cc_start: 0.8383 (tttt) cc_final: 0.7532 (pptt) REVERT: F 317 LYS cc_start: 0.8368 (ptpt) cc_final: 0.7948 (ptmt) REVERT: F 331 LYS cc_start: 0.8883 (mttp) cc_final: 0.8631 (mtpt) REVERT: F 340 LYS cc_start: 0.8667 (mttt) cc_final: 0.8265 (mttp) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 1.4353 time to fit residues: 139.5437 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.144016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.124396 restraints weight = 4147.956| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.45 r_work: 0.3849 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3576 Z= 0.289 Angle : 0.676 9.509 4782 Z= 0.314 Chirality : 0.052 0.143 534 Planarity : 0.004 0.044 612 Dihedral : 4.783 33.101 476 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.49 % Allowed : 24.63 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.017 0.002 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.427 Fit side-chains REVERT: A 311 LYS cc_start: 0.8217 (tttt) cc_final: 0.7872 (ttpt) REVERT: A 317 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7860 (ptmt) REVERT: A 331 LYS cc_start: 0.8613 (mttp) cc_final: 0.8290 (mtpm) REVERT: A 375 LYS cc_start: 0.8211 (tttt) cc_final: 0.7553 (mttm) REVERT: B 311 LYS cc_start: 0.8266 (tttt) cc_final: 0.7760 (mmtt) REVERT: B 317 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8054 (ptmt) REVERT: B 331 LYS cc_start: 0.8699 (mttp) cc_final: 0.8319 (mtpt) REVERT: B 358 ASP cc_start: 0.8683 (p0) cc_final: 0.8299 (p0) REVERT: C 311 LYS cc_start: 0.8327 (tttt) cc_final: 0.7836 (mmtt) REVERT: C 317 LYS cc_start: 0.8363 (ptpp) cc_final: 0.7905 (ptmt) REVERT: C 331 LYS cc_start: 0.8826 (mttp) cc_final: 0.8328 (mtpt) REVERT: C 356 SER cc_start: 0.8813 (p) cc_final: 0.8565 (m) REVERT: C 375 LYS cc_start: 0.8047 (tttt) cc_final: 0.7352 (mttp) REVERT: D 311 LYS cc_start: 0.8451 (tttt) cc_final: 0.7570 (pptt) REVERT: D 317 LYS cc_start: 0.8592 (ptpp) cc_final: 0.7988 (ptmt) REVERT: D 331 LYS cc_start: 0.8881 (mttp) cc_final: 0.8370 (mtpt) REVERT: D 340 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8542 (mttp) REVERT: D 349 ARG cc_start: 0.7645 (ptm160) cc_final: 0.5247 (ppt170) REVERT: D 353 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8473 (ttpp) REVERT: D 375 LYS cc_start: 0.8578 (tttt) cc_final: 0.7995 (mttp) REVERT: E 311 LYS cc_start: 0.8138 (tttt) cc_final: 0.7803 (ttmt) REVERT: E 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8387 (mtpt) REVERT: E 348 ASP cc_start: 0.7711 (t0) cc_final: 0.7396 (m-30) REVERT: F 311 LYS cc_start: 0.8427 (tttt) cc_final: 0.7563 (pptt) REVERT: F 317 LYS cc_start: 0.8470 (ptpt) cc_final: 0.8208 (ptmt) REVERT: F 331 LYS cc_start: 0.8957 (mttp) cc_final: 0.8684 (mtpt) REVERT: F 338 GLU cc_start: 0.8539 (tt0) cc_final: 0.8327 (tt0) REVERT: F 340 LYS cc_start: 0.8693 (mttt) cc_final: 0.8292 (mttp) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 1.4693 time to fit residues: 156.1941 Evaluate side-chains 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.137189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.117517 restraints weight = 4253.027| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.44 r_work: 0.3762 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 3576 Z= 0.547 Angle : 0.785 9.573 4782 Z= 0.380 Chirality : 0.056 0.168 534 Planarity : 0.004 0.042 612 Dihedral : 5.317 28.975 476 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.49 % Allowed : 25.12 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.030 0.004 PHE E 346 TYR 0.025 0.006 TYR F 310 ARG 0.002 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.85 seconds wall clock time: 62 minutes 52.24 seconds (3772.24 seconds total)